When I use any application and I click it shows Not Responding for a second. It doesn't sound like a big deal, but sometimes I need to click twice or even a third time to click on button. Half of the programs end up not responding at all; even when I try to close them they stay open in Task Manager.

Dragging objects is also impossible.

Here's what I've tried so far:

Recovering over the system disc

Windows Recovery doesn't have a point to restore

Setting ALL services on Services list to Automatic start

Reinstalling some of the programs

Registry cleaning and defragmenting

Disk defragmenting

Antivirus scanning

Installing all the latest Windows Updates

UPDATE:

Checked for Malware with 3 different anti-malware programs ( including one in comment )

1-Click Tune Up checked - no errors

Hard Disk Check done

Memory test ( application suggested in comment ) - no errors

Drivers Updates checked - No newer updates

Still not working...

None of these are working. The only thing left is a full system reinstall, meaning delete all data and installing a fresh copy, but as I said at the beginning I have a project I am working on, so I can't do that.

Not touching windows services is best you can do, neither enabling them nor disabling. Since you recovered your system disk, looks like hardware problems. Do the steps HaydnWVN recommended.
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Jens EratNov 4 '11 at 10:50

This sort of error sounds to me like it is some sort of hardware failure, or possibly an interrupt or similar that is causing random freezes.

For hardware failure, check out @HaydnWVN's answer. For interrupt/driver issues:

I first recommend you update all your drivers, especially motherboard/chipset ones. Firstly take a look at your motherboard manufacturers website, and after that if you are still having issues, or if they do not have up to date versions, take a look at the actual silicon vendor webpages (e.g. Realtek and Intel).

After this, if you are still having issues uninstall any specialised programs that install drivers such as Virtual CD programs.

Please let me know if this helps, and if it doesn't, I will try to get in to some more advanced diagnostic steps.